On 9/30/13 2:23 PM, Ehsan Sadeghi wrote:
Yes, I have introduced the new .rtp entry in
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp.
What could be wrong?
The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would
not throw that error. Can you provide the output of:
grep LIG /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
-Justin
----- Original Message -----
From: "Justin Lemkul" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Monday, September 30, 2013 11:16:57 AM
Subject: Re: [gmx-users] ionomer topolgy
On 9/30/13 12:50 PM, Ehsan Sadeghi wrote:
Thanks Justin,
I modified the pdb file, but it cannot recognize my residue LIG. Here is the
error:
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion5.pdb...
Read 46 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 2 residues with 46 atoms
chain #res #atoms
1 ' ' 2 46
All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 108
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.41#
Processing chain 1 (46 atoms, 2 residues)
Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.3
Source code file:
/home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642
Fatal error:
Residue 'LIG' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
You have introduced the new .rtp entry in the correct file, right? That is, you
have modified /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
